Running on a cluster (HPC)

Connectome Mapper 3 BIDS App can be run on a cluster using Singularity.

For your convenience, the Singularity image is automatically built along the docker image using Singularity 3.5.1 and deployed to as (equivalent of DockerHub for Singularity) during continuous integration on CircleCI. It can be freely downloaded with the following command:

$ singularity pull library://connectomicslab/default/connectomemapper-bidsapp:v3.0.0-RC2

If you prefer, you can still build the Singularity image on your side using one of the 2 methods described in Conversion to a Singularity image.

A list of useful singularity command can be found in Useful singularity commands. For more documentation about Singularity, please check the official documentation website.

Running the singularity image

The following example shows how to call from the terminal the Singularity image of the CMP3 BIDS App to perform both anatomical and diffusion pipelines for sub-01, sub-02 and sub-03 of a BIDS dataset whose root directory is located at ${localDir}:

$ singularity run --containall \
    --bind ${localDir}:/bids_dir --bind ${localDir}/derivatives:/output_dir \
        library://connectomicslab/default/connectomemapper-bidsapp:v3.0.0-RC2 \
        /bids_dir /output_dir participant --participant_label 01 02 03 \
        --anat_pipeline_config /bids_dir/code/ref_anatomical_config.ini \
        --dwi_pipeline_config /bids_dir/code/ref_diffusion_config.ini \
        --fs_license /bids_dir/code/license.txt \
        --number_of_participants_processed_in_parallel 3


As you can see, the singularity run command is slightly different from the docker run. The docker option flag -v is replaced by the singularity --bind to map local folders inside the container. Last but not least, while docker containers are executed in total isolation, singularity images MUST run with the option flag --containall. Otherwise your $HOME and $TMP directories or your local environment variables might be shared inside the container.

Conversion to a Singularity image

It actually exists two options for Docker to Singularity container image conversion. Let’s say we want to store Singularity-compatible image file in ~/Softwares/singularity/.

Option 2 : Using singularity directly

$ singularity build ~/Softwares/singularity/cmp-v3.0.0-RC2.simg docker://sebastientourbier/connectomemapper-bidsapp:v3.0.0-RC2

This command will directly download the latest version release of the Docker image from the DockerHub and convert it to a Singularity image.

Advantage(s): Can be executed on the cluster directly

Disadvantage(s): Has shown to fail because of some docker/ singularity version uncompatibilities

Useful singularity commands

  • Display a container’s metadata:

    $ singularity inspect ~/Softwares/singularity/cmp-v3.0.0-RC2.simg
  • Clean cache:

    $ singularity cache clean

Created by Sebastien Tourbier - 2020 Mar 04 - Latest update: 2020 Dec 24